I think they would attack though,they (Stormcloaks) are also at a weakened stage which i guess is the BEST time to attack.You are still outnumbered
It will be good to get rid of the sun though, vampires would rule the earth except that erh.. the whole mankind rises to arms against them
Edit: I would kill selena,harkon and every single of those damn bastards after i get this damn auriel's bow (Stuck at the Frost giant, getting to the last wayshrine)
Okay, found the way and finish the quest, also killed harkon, i don't seem to have a choice though?